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Benchmarking ultra-...
Benchmarking ultra-high molecular weight DNA preservation methods for long-read and long-range sequencing
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- Dahn, Hollis A. (author)
- Univ Toronto, Dept Ecol & Evolutionary Biol, Toronto, ON M5S 3B2, Canada.
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- Mountcastle, Jacquelyn (author)
- Rockefeller Univ, New York, NY 10065 USA.
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- Balacco, Jennifer (author)
- Rockefeller Univ, New York, NY 10065 USA.
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- Winkler, Sylke (author)
- Max Planck Inst Mol Cell Biol & Genet, D-01307 Saxony, Germany.
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- Bista, Iliana (author)
- Wellcome Sanger Inst, Tree Life Program, Hinxton CB10 1SA, Cambs, England.;Univ Cambridge, Dept Genet, Cambridge CB2 3EH, Cambs, England.
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- Schmitt, Anthony D. (author)
- Arima Genom Inc, San Diego, CA 92121 USA.
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- Vinnere, Olga (author)
- Uppsala universitet,Institutionen för immunologi, genetik och patologi,Science for Life Laboratory, SciLifeLab
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- Formenti, Giulio (author)
- Rockefeller Univ, New York, NY 10065 USA.
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- Oliver, Karen (author)
- Wellcome Sanger Inst, Tree Life Program, Hinxton CB10 1SA, Cambs, England.
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- Smith, Michelle (author)
- Wellcome Sanger Inst, Tree Life Program, Hinxton CB10 1SA, Cambs, England.
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- Tan, Wenhua (author)
- Max Planck Inst Mol Cell Biol & Genet, D-01307 Saxony, Germany.
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- Kraus, Anne (author)
- Max Planck Inst Mol Cell Biol & Genet, D-01307 Saxony, Germany.
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- Mac, Stephen (author)
- Arima Genom Inc, San Diego, CA 92121 USA.
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- Komoroske, Lisa M. (author)
- Univ Massachusetts, Dept Environm Conservat, Amherst, MA 01003 USA.
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- Lama, Tanya (author)
- Univ Massachusetts, Dept Environm Conservat, Amherst, MA 01003 USA.
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- Crawford, Andrew J. (author)
- Univ Los Andes, Dept Biol Sci, Bogota 111711, Colombia.
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- Murphy, Robert W. (author)
- Univ Toronto, Dept Ecol & Evolutionary Biol, Toronto, ON M5S 3B2, Canada.
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- Brown, Samara (author)
- Rockefeller Univ, New York, NY 10065 USA.
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- Scott, Alan F. (author)
- Johns Hopkins Univ, Dept Med, Baltimore, MD 21287 USA.
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- Morin, Phillip A. (author)
- NOAA, Southwest Fisheries Sci Ctr, Natl Marine Fisheries Serv, La Jolla, CA 92037 USA.
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- Jarvis, Erich D. (author)
- Rockefeller Univ, New York, NY 10065 USA.;Howard Hughes Med Inst, Chevy Chase, MD 20815 USA.
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- Fedrigo, Olivier (author)
- Rockefeller Univ, New York, NY 10065 USA.
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Univ Toronto, Dept Ecol & Evolutionary Biol, Toronto, ON M5S 3B2, Canada Rockefeller Univ, New York, NY 10065 USA. (creator_code:org_t)
- 2022-08-10
- 2022
- English.
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In: GigaScience. - : Oxford University Press. - 2047-217X. ; 11
- Related links:
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Abstract
Subject headings
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- Background: Studies in vertebrate genomics require sampling from a broad range of tissue types, taxa, and localities. Recent advancements in long-read and long-range genome sequencing have made it possible to produce high-quality chromosome-level genome assemblies for almost any organism. However, adequate tissue preservation for the requisite ultra-high molecular weight DNA (uHMW DNA) remains a major challenge. Here we present a comparative study of preservation methods for field and laboratory tissue sampling, across vertebrate classes and different tissue types.Results: We find that storage temperature was the strongest predictor of uHMW fragment lengths. While immediate flash-freezing remains the sample preservation gold standard, samples preserved in 95% EtOH or 20-25% DMSO-EDTA showed little fragment length degradation when stored at 4 degrees C for 6 hours. Samples in 95% EtOH or 20-25% DMSO-EDTA kept at 4 degrees C for 1 week after dissection still yielded adequate amounts of uHMW DNA for most applications. Tissue type was a significant predictor of total DNA yield but not fragment length. Preservation solution had a smaller but significant influence on both fragment length and DNA yield.Conclusion: We provide sample preservation guidelines that ensure sufficient DNA integrity and amount required for use with long-read and long-range sequencing technologies across vertebrates. Our best practices generated the uHMW DNA needed for the high-quality reference genomes for phase 1 of the Vertebrate Genomes Project, whose ultimate mission is to generate chromosome-level reference genome assemblies of all similar to 70,000 extant vertebrate species.
Subject headings
- NATURVETENSKAP -- Biologi -- Genetik (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Genetics (hsv//eng)
Keyword
- long-read sequencing
- genome assembly
- tissue preservation
- HMW DNA extraction
Publication and Content Type
- ref (subject category)
- art (subject category)
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- By the author/editor
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Dahn, Hollis A.
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Mountcastle, Jac ...
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Balacco, Jennife ...
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Winkler, Sylke
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Bista, Iliana
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Schmitt, Anthony ...
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show more...
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Vinnere, Olga
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Formenti, Giulio
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Oliver, Karen
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Smith, Michelle
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Tan, Wenhua
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Kraus, Anne
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Mac, Stephen
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Komoroske, Lisa ...
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Lama, Tanya
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Crawford, Andrew ...
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Murphy, Robert W ...
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Brown, Samara
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Scott, Alan F.
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Morin, Phillip A ...
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Jarvis, Erich D.
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Fedrigo, Olivier
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- About the subject
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- NATURAL SCIENCES
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NATURAL SCIENCES
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and Biological Scien ...
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and Genetics
- Articles in the publication
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GigaScience
- By the university
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Uppsala University